IMP GPI Lipid Anchor Project IMP-Bioinformatics

The self-consistency-test of the learning set for Protozoa

Contact:
Birgit Eisenhaber (IMP/Austria)
Peer Bork (MDC/EMBL)
Frank Eisenhaber (IMP/Austria)


Description of Prediction Function
Prediction Results
How to read the prediction results

#
# ------------------------------------------------------------------- #
# 
# package *-> proto <-*
# *********************
# 
# name of executable           : proto
# time of program compilation  : Apr 14 1999 (15:43:37)
# time of program execution    : Wed Apr 14 15:56:51 1999
# version of the code          : Revision: 1.15 (Date: 1999/01/28 15:56:41)
# 
ReadAapLib: AAProperty library  opened
Number of entrys in AapLib: <641>
-->All selects were switched on.


Selection parameters:
---------------------
0:     PToken: OC   
       SToken: 
         RExp: PROTOZOA
    is_SToken: 0
       expect: 1

-->OpenSWFile: Data file <./gpi.learn.sav> opened

-->begin GPI-site evaluations
-->ReadGPILib: GPI library  opened
 INFO> ReadGPILib: VARSPLIC line in entry <UPAR_RAT> .!!
 INFO> ReadGPILib: VARSPLIC line in entry <ACES_TORCA> .!!
 INFO> ReadGPILib: VARSPLIC line in entry <ACES_TORMA> .!!
 INFO> ReadGPILib: VARSPLIC line in entry <CEPU_CHICK> .!!
 INFO> ReadGPILib: VARSPLIC line in entry <DAF_HUMAN> .!!
 INFO> ReadGPILib: VARSPLIC line in entry <NRTR_HUMAN> .!!
 INFO> ReadGPILib: VARSPLIC line in entry <NRTR_MOUSE> .!!
 INFO> ReadGPILib: VARSPLIC line in entry <OPCM_RAT> .!!
number of entries of file 1                   :   169
number of accepted entries of file 1          :   169
total number of entries                       :   169

-->Statistic_confidence of GPILib 1 : 
number of accepted entries                    :   169
number of entries with certain GPI-site       :    40
number of entries with potential GPI-site     :    65
number of entries with GPI-site by similarity :    64

-->GPIStatistic_Length: GPILibNumber = 1
Lmin                :  14 ( entry: PAG1_TRYBB, file: 1 )
Lmax                :  31 ( entry: THY1_MACMU, file: 1 )
deltaL              :   5
number of intervals :   4
interval of length   from     to    number of entries
                 1     14     19                   21
                 2     20     24                   84
                 3     25     29                   53
                 4     30     34                   11
total number of entries                       :   169

-->Statistic_taxonomy of GPILib 1 / total number of entries 169
     1 VIRIDAE
   168 EUKARYOTA
   120 ..METAZOA
     5 ....INSECTA
   113 ....VERTEBRATA
     3 ......PISCES
     5 ......AVES
   105 ......MAMMALIA
    55 ........PRIMATES
    10 ..FUNGI
    38 ..PROTOZOA

-->Calc_EVD_Param: file of values  opened
LinearCorrelation of 1061 data points [x,y]
           r=-0.975986 (P=0.000000)

LinearFit: from 1061 datapoints [x,y] for y=a+bx (1059 degrees of freedom)
           without weights (RMSD) for y (uniform sigma is estimated)
           x mean=-75.462328 (stan.dev.=24.061508)
           y mean=-0.574634 (stan.dev.=1.269734)
           interception a=-4.461182	(siga=0.027977)
           slope        b=-0.051503	(sigb=0.000353)
           correlation  R(siga,sigb)=0.952782

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ > statistical validation
        1) total chi2=81.090823,	P=1.000000e+00 B=-ln(P)/df= 0.000
           (used for weight estimation !)

        2) t-Test for interception a=0: t=-159.459749	P=0.000000e+00
           [-4.553500,-4.368863] for alpha=0.001 (TWO_SIDED, Tna=3.299805)
           [-4.533376,-4.388987] for alpha=0.010 (TWO_SIDED, Tna=2.580505)
           [-4.516078,-4.406285] for alpha=0.050 (TWO_SIDED, Tna=1.962204)

        3) t-Test for slope        b=0: t=-145.804769	P=0.000000e+00
           [-0.052669,-0.050338] for alpha=0.001 (TWO_SIDED, Tna=3.299805)
           [-0.052415,-0.050592] for alpha=0.010 (TWO_SIDED, Tna=2.580505)
           [-0.052196,-0.050810] for alpha=0.050 (TWO_SIDED, Tna=1.962204)

        4) Fisher's test (average of function value versus regression)
           F=21259.030543 (df1=1, df2=1059) P=0.000000e+00

   u: -86.619580 lambda: 0.051503
Thresholds for GPI-anchor selecting:
   A-site: p = 0.0025 score =  29.69
   B-site: p = 0.0050 score =  16.21
   C-site: p = 0.0075 score =   8.31
   D-site: p = 0.0100 score =   2.70
   S-site: p = 0.0175 score =  -8.24

-->All flags of selected entries were switched on.

-->Switch_Off_Tax: number of entries before procedure : 169
-->Flags of all entries except PROTOZOA switched off
-->Switch_Off_Tax: number of entries after procedure : 38

-->Switch_Off_Len: number of entries before procedure : 38
-->Flags of all entries with AALen-GPIPos > 31 switched off
-->Flags of all entries with AALen-GPIPos < 17 switched off
-->Switch_Off_Len: number of entries after procedure : 37

possible largest subset found: Q =   29
possible largest subset found: Q =   19
largest subset found: q = 19
number of 0's in found largest subset: 0
-->Mean and Dispersion of property <NAKH920105> from 3 to 8
   Mean: 7.426140
   Dispersion: 2.057393
-->Mean and Dispersion of property <NAKH920105> from 10 to SEQUENCE_CEND
   Mean: 12.707411
   Dispersion: 2.079704
-->Mean and Dispersion of property <NAKH920105> from 26 to SEQUENCE_CEND
   Mean: 12.954671
   Dispersion: 1.923591
-->Mean and Dispersion of property <HAGECH94_V> from 3 to 8
   Mean: 138.192105
   Dispersion: 17.443998
-->Mean and Dispersion of property <HAGECH94_V> at position(s) -1 0 1 2 
   number of selected entries: 19
   Mean : 418.015789
   Dispersion:  53.808212
-->Mean and Dispersion of property <HAGECH94_V> at position(s) -1 1 2 
   number of selected entries: 19
   Mean : 317.368421
   Dispersion:  49.519806
-->Mean and Dispersion of property <HAGECH94_V> at position(s) -1 2 
   number of selected entries: 19
   Mean : 211.873684
   Dispersion:  43.480977

-->All flags of selected entries were switched on.

-->Switch_Off_Tax: number of entries before procedure : 169
-->Flags of all entries except PROTOZOA switched off
-->Switch_Off_Tax: number of entries after procedure : 38

-->Switch_Off_Len: number of entries before procedure : 38
-->Flags of all entries with AALen-GPIPos > 31 switched off
-->Flags of all entries with AALen-GPIPos < 17 switched off
-->Switch_Off_Len: number of entries after procedure : 37

NSubFam = 6
Profile:
Ala
 -3.8  -0.1  -3.6  -0.1  -0.9  -0.9  -0.7  -0.7  -0.8   0.5   0.8  -3.8   0.1  -0.6  -3.6 
  0.1   0.2   1.4   0.5  -0.6  -0.6  -0.7  -0.5   0.8  -3.7   1.3   0.6   0.5   0.9   1.1 
  0.5   1.4   1.3   0.6   1.4   1.3   0.8   0.9   0.2   1.6  -2.5 
Cys
  1.7   1.7   0.7   1.3  -3.6  -3.7   2.3   0.7  -3.7  -3.5  -3.4   0.8  -3.5   2.7   0.8 
 -3.9  -3.7  -3.8  -3.4  -3.4  -3.6  -3.7  -3.5  -3.6  -3.7  -3.5  -3.6  -3.7  -3.7  -3.8 
 -3.8   0.9  -3.7  -3.6  -3.7  -3.6   1.2  -3.5  -3.2  -2.6  -2.5 
Asp
  0.7  -0.4  -0.3   0.3   0.6   0.7   0.5   0.9  -3.7   0.4  -3.4  -0.3   1.2  -0.2  -0.2 
  1.5   0.6   0.0  -3.4  -3.4  -3.6  -3.7  -3.5  -3.6  -3.7  -3.5  -3.6  -3.7  -3.7  -3.8 
 -0.2  -3.8  -3.7  -3.6  -3.7  -3.6  -3.8  -3.5  -3.2  -2.6  -2.5 
Glu
  0.5   1.2   0.3   1.2   0.1   0.8   0.3   0.7  -0.5   1.7   0.0   1.6   0.3  -0.2  -3.6 
 -3.9  -3.7  -3.8  -3.4  -3.4  -3.6  -3.7  -3.5  -3.6  -3.7  -3.5  -3.6  -3.7  -3.7  -3.8 
 -3.8  -3.8  -3.7  -3.6  -3.7  -3.6  -3.8  -3.5  -3.2  -2.6  -2.5 
Phe
 -3.8  -3.8  -3.6  -3.6  -3.6  -3.7  -3.5  -3.5  -3.7  -3.5  -3.4  -3.8  -3.5  -3.4  -3.6 
 -3.9   0.2  -3.8   1.7  -3.4  -3.6  -3.7   0.2  -3.6   2.0   0.1   0.9   0.1   0.1   1.3 
  0.1   1.5   1.5   2.2  -3.7   0.4   1.1   1.7   2.6  -2.6   2.5 
Gly
  0.4   1.0  -0.6  -0.7   0.7   0.6  -0.6   0.6   0.5  -3.5   0.9   0.1  -0.5   1.0   1.3 
  0.7   0.9  -3.8   0.3   0.2   0.2  -3.7   0.7  -3.6  -0.5  -3.5  -0.4  -3.7  -3.7  -3.8 
 -3.8  -0.5  -0.5  -3.6  -3.7  -3.6  -3.8  -3.5  -3.2  -2.6  -2.5 
His
 -3.8  -3.8   0.6  -3.6  -3.6  -3.7   0.6  -3.5  -3.7  -3.5  -3.4  -3.8   0.7  -3.4  -3.6 
 -3.9  -3.7  -3.8  -3.4   0.7  -3.6   0.6  -3.5  -3.6  -3.7  -3.5  -3.6  -3.7  -3.7   0.7 
 -3.8  -3.8  -3.7  -3.6  -3.7  -3.6  -3.8   1.1  -3.2  -2.6  -2.5 
Ile
 -3.8  -3.8  -3.6  -3.6  -3.6  -3.7  -3.5  -0.4  -3.7  -0.3  -0.3  -0.3  -3.5  -3.4  -3.6 
 -3.9  -3.7  -3.8   1.3  -0.2   0.9  -0.3  -3.5  -0.3  -0.2  -3.5  -0.2   1.0   0.5   0.4 
 -3.8   0.5   0.4   0.0  -3.7  -3.6  -3.8   0.9  -3.2  -2.6  -2.5 
Lys
  0.5   0.8   1.4   0.1   0.1   0.9   0.3   1.0   0.3   0.4   0.3   0.7   0.5  -3.4   1.1 
 -3.9  -3.7  -3.8  -3.4  -0.3   0.4   0.8   1.8   0.5  -3.7  -3.5  -3.6  -3.7  -3.7  -3.8 
 -3.8  -3.8  -3.7  -3.6  -3.7  -3.6  -3.8  -3.5  -3.2  -2.6  -2.5 
Leu
 -3.8  -0.9  -3.6  -3.6  -3.6  -3.7  -3.5  -3.5  -3.7  -3.5  -0.8  -3.8  -3.5  -0.7  -3.6 
 -3.9  -3.7  -0.6  -0.7   1.3   0.7  -3.7  -3.5  -0.8   1.1   0.7   1.5   0.7   0.4   0.4 
  1.5   0.9   0.6   1.2   0.5   1.6   1.9   1.3   0.0   0.7   1.6 
Met
 -3.8  -3.8  -3.6  -3.6  -3.6  -3.7  -3.5  -3.5  -3.7  -3.5   0.5  -3.8  -3.5  -3.4  -3.6 
 -3.9  -3.7  -3.8  -3.4  -3.4  -3.6  -3.7   0.6  -3.6  -3.7  -3.5  -3.6   1.2   0.6  -3.8 
 -3.8   0.6  -3.7  -3.6   1.7  -3.6  -3.8  -3.5  -3.2  -2.6  -2.5 
Asn
 -3.8   0.5  -0.1   0.5  -0.3   0.9   1.0  -3.5   0.6  -3.5   0.9   1.0   0.0   0.0  -3.6 
  1.4   1.3  -3.8  -3.4  -3.4  -3.6   1.5  -3.5  -0.1  -3.7  -3.5  -3.6  -3.7  -3.7  -3.8 
 -3.8  -3.8  -3.7  -3.6  -3.7  -3.6  -3.8  -3.5  -3.2  -2.6  -2.5 
Pro
  1.0  -3.8   1.0  -0.4   1.4   1.0   1.1  -0.3   1.3  -3.5   0.8  -3.8  -0.1  -3.4   1.2 
 -3.9  -3.7  -3.8  -0.1  -0.1  -3.6  -3.7  -3.5   0.9   1.1   0.6  -3.6  -3.7  -3.7  -3.8 
 -0.2  -3.8  -3.7  -3.6  -3.7  -3.6  -3.8  -3.5  -3.2  -2.6  -2.5 
Gln
 -0.2  -3.8   0.7  -3.6   0.9  -3.7   0.0  -3.5   1.0   0.0  -3.4  -3.8   0.1  -3.4   0.1 
 -3.9  -3.7  -3.8  -3.4  -3.4  -3.6  -3.7  -3.5   1.5  -3.7  -3.5  -3.6  -3.7  -3.7  -3.8 
 -3.8  -3.8  -3.7  -3.6   0.3   0.3  -3.8  -3.5   0.9   1.6  -2.5 
Arg
 -3.8  -3.8  -0.4   0.2  -0.6  -0.5  -3.5  -3.5  -3.7  -0.4  -3.4  -3.8  -0.3  -3.4   0.4 
 -3.9  -3.7  -3.8  -0.2  -3.4   0.4   0.3  -0.2  -3.6   0.4  -0.3  -3.6  -3.7  -3.7  -3.8 
 -3.8  -3.8  -3.7  -3.6  -3.7  -3.6  -3.8  -3.5  -3.2  -2.6  -2.5 
Ser
  0.0  -3.8  -3.6   0.9   0.7  -3.7   0.1   0.5   0.5   0.2  -0.6  -0.1  -3.5   0.3   0.3 
  1.6   1.5   2.1   0.6   0.2  -3.6   1.3   0.3   1.1  -3.7   1.0  -0.4   1.4   0.2  -0.5 
  1.4  -3.8  -0.5  -0.3  -0.3  -0.2  -3.8  -3.5  -3.2  -2.6  -2.5 
Thr
  1.0   0.9   0.9   0.8   0.6   0.9   0.1   0.7   0.3   0.8   0.8   1.3   1.6   0.9  -0.3 
 -3.9   0.5  -3.8   0.5   0.8   1.1   0.8   1.0   0.3  -0.3  -0.3  -3.6  -0.3   0.8  -3.8 
 -3.8  -3.8   0.3  -3.6  -3.7  -0.1  -3.8   0.1  -3.2   1.2  -2.5 
Val
  0.4  -3.8   0.1  -3.6  -3.6  -0.7  -3.5   0.1  -3.7  -0.5  -3.4  -3.8  -3.5   0.3  -0.5 
 -3.9  -3.7  -3.8  -3.4   0.7   1.0   0.2  -0.3  -3.6  -0.4  -0.4  -0.4   0.2   1.4   1.1 
 -0.5  -0.4   0.6  -0.2   1.4  -3.6  -3.8  -3.5   1.0  -2.6  -2.5 
Trp
 -3.8  -3.8  -3.6  -3.6  -3.6  -3.7  -3.5  -3.5   2.5  -3.5  -3.4  -3.8  -3.5  -3.4  -3.6 
 -3.9  -3.7  -3.8  -3.4  -3.4  -3.6  -3.7  -3.5  -3.6  -3.7  -3.5   2.3  -3.7  -3.7  -3.8 
 -3.8  -3.8  -3.7   1.4  -3.7  -3.6  -3.8  -3.5  -3.2  -2.6  -2.5 
Tyr
 -3.8  -3.8  -3.6  -3.6  -3.6  -3.7  -3.5  -3.5  -3.7  -3.5  -3.4  -3.8  -3.5  -3.4  -3.6 
 -3.9  -3.7  -3.8  -3.4  -3.4  -3.6  -3.7  -3.5  -3.6  -3.7   0.3  -3.6  -3.7  -3.7   1.0 
 -3.8  -3.8  -3.7  -3.6  -3.7  -3.6  -3.8  -3.5  -3.2  -2.6  -2.5 

ConsensSequence: t e k e p e c k p e a e t c g s s S f l l s k s f a l s v a l a a f a l L l F a f

Positions with profile component > 1.0 for all amino acid types
Ala  2 10 14 16 17 19 20 24
Cys  -15 -14 -12 -9 -2 21
Asp  -3 0
Glu  -14 -12 -6 -4
Phe  3 9 14 16 17 18 21 22 23 25
Gly  -1
His  22
Ile  3
Lys  -13 -8 -1 7
Leu  4 9 11 15 18 20 21 22 25
Met  12 19
Asn  0 1 6
Pro  -13 -11 -10 -9 -7 -1 9
Gln  -7 8 24
Arg 
Ser  0 1 2 6 8 12 15
Thr  -4 -3 5 24
Val  5 13 14 19 23
Trp  -7 11 18
Tyr 

Parameters for score calculation:
---------------------------------
TaxonCode: 40
Calculation of profile:
   number of input sequences: 37
   number of regions: 5
   1: from                :  -15
      to                  :  -12
      weight of region    :  0.0
   2: from                :  -11
      to                  :   -2
      weight of region    :  0.5
   3: from                :   -1
      to                  :    2
      weight of region    :  3.0
   4: from                :    3
      to                  :    9
      weight of region    :  0.5
   5: from                :   10
      to                  :   25
      weight of region    :  1.0
   weight of profile      :  0.6
omega-site will be searched in interval [10..40] from C-terminal

Function 0 = Sum : volume function
   Parameters:
   ScFunc[0].from         =            -1
   ScFunc[0].to           =             2
   ScFunc[0].PropertyName =    HAGECH94_V mean volume of residues
   ScFunc[0].par1         =        418.02 mean volume was calculated
   ScFunc[0].par2         =         53.81 dispersion was calculated
   ScFunc[0].wfunc        =          1.00
   ScFunc[0].distr_type   =       F_GAUSS

Function 1 = Sum3 : volume function for three positions
   Parameters:
   ScFunc[1].from         =            -1 Position 1
   ScFunc[1].to           =             0 Position 2
   ScFunc[1].PropertyName =    HAGECH94_V mean volume of residues
   ScFunc[1].par1         =        317.37 mean volume was calculated
   ScFunc[1].par2         =         49.52 dispersion was calculated
   ScFunc[1].par4         =             1 Position 3
   ScFunc[1].wfunc        =          1.00
   ScFunc[1].distr_type   =       F_GAUSS

Function 2 = Sum2 : volume function for two positions
   Parameters:
   ScFunc[2].from         =            -1 Position 1
   ScFunc[2].to           =             1 Position 2
   ScFunc[2].PropertyName =    HAGECH94_V mean volume of residues
   ScFunc[2].par1         =        211.87 mean volume was calculated
   ScFunc[2].par2         =         43.48 dispersion was calculated
   ScFunc[2].wfunc        =          1.00
   ScFunc[2].distr_type   =       F_GAUSS

Function 3 = PenaltyForBadProfile : penalty for bad Omega-Site
   Parameters:
   ScFunc[3].from         =             0
   ScFunc[3].to           =             2
   ScFunc[3].par1         =          0.10 threshold
   ScFunc[3].par2         =         -4.00 penalty
   ScFunc[3].wfunc        =          1.00

Function 4 = Penalty_Mobility : penalty for more than one residue out of P, T, V, I
   Parameters:
   ScFunc[4].from         =            -1 Position 1
   ScFunc[4].to           =             2 Position 2
   ScFunc[4].PropertyName =    PTVI residues
   ScFunc[4].par1         =         -4.00 penalty
   ScFunc[4].wfunc        =          1.00

Function 5 = C_Position : penalty, if site is outside of interval[from..to] relative to C-terminal
   Parameters:
   ScFunc[5].from         =            17
   ScFunc[5].to           =            31
   ScFunc[5].par1         =          1.00 lambda (x < from)
   ScFunc[5].par2         =          1.00 lambda (x > to)
   ScFunc[5].wfunc        =          4.00
   ScFunc[5].distr_type   =   F_BOLTZMANN

Function 6 = Lower_Average : function for hydrophophilic spacer(for positions 3..8)
   Parameters:
   ScFunc[6].from         =             3 (after omega-site)
   ScFunc[6].to           =             8
   ScFunc[6].PropertyName =    NAKH920105 hydrophobicity scale
   ScFunc[6].par1         =          7.43 mean hydrophobicity for spacer region was calculated
   ScFunc[6].par2         =          2.06 dispersion was calculated
   ScFunc[6].wfunc        =          3.00
   ScFunc[6].distr_type   =       F_GAUSS

Function 7 = Lower_Average : function for spacer volume (mean for positions 3..8)
   Parameters:
   ScFunc[7].from         =             3 (after omega-site)
   ScFunc[7].to           =             8
   ScFunc[7].PropertyName =    HAGECH94_V mean volume of residues
   ScFunc[7].par1         =        138.19 mean volume for spacer region was calculated
   ScFunc[7].par2         =         17.44 dispersion was calculated
   ScFunc[7].wfunc        =          1.00
   ScFunc[7].distr_type   =       F_GAUSS

 Function 8 = Higher_Average: function for hydrophobic region [10..C_end] (for at least the par4=8 last AA)
   Parameters:
   ScFunc[8].from         =            10
   ScFunc[8].to           = SEQUENCE_CEND
   ScFunc[8].PropertyName =    NAKH920105 hydrophobicity scale
   ScFunc[8].par1         =         12.71 mean hydrophobicity for at least the 8 last AA was calculated
   ScFunc[8].par2         =          2.08 dispersion was calculated
   ScFunc[8].par4         =             8 minimal length of hydrophobic region
   ScFunc[8].wfunc        =          1.00
   ScFunc[8].distr_type   =       F_GAUSS

Function 9 = Higher_Average : function for hydrophobic tail [25..C_end](for at least the par4=8 last AA)
   Parameters:
   ScFunc[9].from         =            26 (after profile-end)
   ScFunc[9].to           = SEQUENCE_CEND
   ScFunc[9].PropertyName =    NAKH920105 hydrophobicity scale
   ScFunc[9].par1         =         12.95 mean hydrophobicity for at least the 8 last AA was calculated
   ScFunc[9].par2         =          1.92 dispersion was calculated
   ScFunc[9].par4         =             8 minimal length of tail for calculation of hydrophobicity parameters
   ScFunc[9].wfunc        =          1.00
   ScFunc[9].distr_type   =       F_GAUSS

Function 10 = Sliding_Window : penalty for too short even hydrophobic section
   Parameters:
   ScFunc[10].from         =             9
   ScFunc[10].to           = SEQUENCE_CEND
   ScFunc[10].PropertyName =    NAKH920105 hydrophobicity scale
   ScFunc[10].par1         =          9.00 threshold ( min mean window hydrophobicity)
   ScFunc[10].par2         =        -12.00 penalty
   ScFunc[10].par4         =             4 winlen
   ScFunc[10].par5         =             5 min number of windows one after another
   ScFunc[10].wfunc        =          1.00

Function 11 = PenaltyForBadProfile : penalty for bad hydrophobic tail
   Parameters:
   ScFunc[11].from         =            10
   ScFunc[11].to           =   PROFILE_END
   ScFunc[11].par1         =          0.10 threshold
   ScFunc[11].par2         =        -12.00 penalty
   ScFunc[11].wfunc        =          1.00

Function 12 = Penalty_Lower : penalty, if hydrophobicity in tail < threshold=par1
   Parameters:
   ScFunc[12].from         =            10 
   ScFunc[12].to           = SEQUENCE_CEND
   ScFunc[12].par1         =          1.50 minimum of mean hydrophobicity (NAKH920105)
   ScFunc[12].par2         =         -4.00 penalty
   ScFunc[12].par3         =          0.50 threshold for extreme windows
   ScFunc[12].par4         =             3 windowlength for calculation of mean hydrophobicity
   ScFunc[12].wfunc        =          1.00

Function 13 =  LVI_contents : contents of Leu, Val, Ile in hydrophobic tail
   Parameters:
   ScFunc[13].from         =            10
   ScFunc[13].to           = SEQUENCE_CEND
   ScFunc[13].par1         =         30.00 threshold
   ScFunc[13].par2         =        -12.00 penalty
   ScFunc[13].wfunc        =          1.00

Function 14 = SG_Penalty : penalty for too long Ser, Gly - sections (len = par4) in hydrophobic tail
   Parameters:
   ScFunc[14].from         =             9
   ScFunc[14].to           = SEQUENCE_CEND
   ScFunc[14].par1         =        -12.00 penalty
   ScFunc[14].par4         =             3 winlen
   ScFunc[14].wfunc        =          1.00
18.95 0.00 0.00 -0.21 0.00 0.00 0.00 0.00 0.00 -0.23 -0.17 0.00 0.00 0.00 0.00 0.00 18.34
ID:
G13B_DICDI AC: P34116 Len: 734 1:B 708 Sc: 18.34
24.14 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 24.14
ID: GP63_LEIMA AC: P08148 Len: 602 1:B 577 Sc: 24.14
29.52 -0.23 -0.38 -0.27 0.00 0.00 0.00 -1.34 -0.52 -0.08 -0.09 0.00 0.00 0.00 0.00 0.00 26.60
ID: VSG7_TRYBR AC: P02898 Len: 467 1:B 444 Sc: 26.60
23.38 0.00 0.00 -0.01 0.00 0.00 0.00 -0.66 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 22.71
ID: CSA_DICDI AC: P08796 Len: 514 1:B 492 Sc: 22.71
21.63 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.04 -0.41 0.00 0.00 0.00 0.00 0.00 21.18
ID: G13A_DICDI AC: P34115 Len: 730 1:B 708 Sc: 21.18
23.59 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 23.59
ID: GP63_LEICH AC: P15706 Len: 599 1:B 574 Sc: 23.59
23.59 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 23.59
ID: GP63_LEIDO AC: P23223 Len: 590 1:B 565 Sc: 23.59
14.08 -1.17 -1.76 -3.11 0.00 0.00 0.00 -2.18 0.00 0.00 -0.14 0.00 0.00 0.00 0.00 0.00 5.71
ID: GP85_TRYCR AC: Q03877 Len: 714 1:D 691 Sc: 5.71
18.07 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.59 0.00 0.00 0.00 0.00 0.00 0.00 17.47
ID: MSA1_SARMU AC: Q01416 Len: 280 1:B 256 Sc: 17.47
-13.30 -0.30 0.00 0.00 -4.00 0.00 0.00 0.00 -0.02 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -17.62
ID: PAG1_TRYBB AC: Q01889 Len: 405 1:N 388 Sc: -17.62
$ site was 391
19.75 0.00 0.00 0.00 0.00 0.00 0.00 -1.11 0.00 -0.60 -0.26 0.00 0.00 0.00 -12.00 0.00 5.78
ID: PARA_TRYBB AC: P18764 Len: 114 1:D 92 Sc: 5.78
17.59 0.00 0.00 0.00 0.00 0.00 0.00 -1.11 0.00 -0.46 -0.15 0.00 0.00 0.00 0.00 0.00 15.87
ID: PARB_TRYBB AC: P09791 Len: 129 1:C 107 Sc: 15.87
19.91 0.00 0.00 0.00 0.00 0.00 0.00 -1.11 0.00 -0.56 -0.26 0.00 0.00 0.00 -12.00 0.00 5.97
ID: PARC_TRYBB AC: Q06084 Len: 145 1:D 123 Sc: 5.97
23.76 0.00 0.00 0.00 0.00 0.00 0.00 -0.12 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 23.64
ID: PONA_DICDI AC: P54660 Len: 143 1:B 118 Sc: 23.64
16.51 0.00 0.00 0.00 0.00 0.00 0.00 -0.44 0.00 -0.22 -1.28 -12.00 0.00 0.00 0.00 0.00 2.57
ID: PSA_DICDI AC: P12729 Len: 168 1:I 147 Sc: 2.57
32.62 -0.57 -0.83 -0.72 0.00 0.00 0.00 -4.21 -0.31 0.00 0.00 0.00 0.00 0.00 0.00 0.00 25.97
ID: VSA1_TRYBB AC: P06015 Len: 503 1:B 480 Sc: 25.97
33.91 -0.57 -0.83 -0.72 0.00 0.00 0.00 -0.85 -0.34 -0.08 -0.09 0.00 0.00 0.00 0.00 0.00 30.43
ID: VSA8_TRYBB AC: P06017 Len: 115 1:A 92 Sc: 30.43
32.23 -0.57 -0.83 -0.72 0.00 0.00 0.00 -1.41 -0.45 -0.05 -0.32 0.00 0.00 0.00 0.00 0.00 27.87
ID: VSAC_TRYBB AC: P06016 Len: 482 1:B 459 Sc: 27.87
21.28 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 21.28
ID: VSE2_TRYBR AC: P26335 Len: 55 1:B 38 Sc: 21.28
23.46 0.00 0.00 0.00 0.00 0.00 0.00 -0.03 -0.44 0.00 0.00 0.00 0.00 0.00 0.00 0.00 22.99
ID: VSG2_TRYEQ AC: P20950 Len: 457 1:B 440 Sc: 22.99
28.10 -0.57 -0.83 -0.72 0.00 0.00 0.00 -0.85 -0.34 -2.54 -5.29 -12.00 0.00 0.00 -12.00 0.00 -7.06
ID: VSG4_TRYBR AC: P02897 Len: 476 1:I 457 Sc: -7.06
17.32 -0.12 -0.22 -0.52 0.00 0.00 0.00 -5.63 -0.11 0.00 0.00 0.00 0.00 0.00 0.00 0.00 10.71
ID: VSI1_TRYBB AC: P26326 Len: 471 1:C 454 Sc: 10.71
21.28 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 21.28
ID: VSI2_TRYBB AC: P26327 Len: 479 1:B 462 Sc: 21.28
23.88 -0.63 -0.91 -0.53 0.00 0.00 0.00 0.00 -0.76 -0.17 -0.31 0.00 0.00 0.00 0.00 0.00 20.58
ID: VSI3_TRYBB AC: P26328 Len: 532 1:B 509 Sc: 20.58
$ site was 511
33.42 -0.57 -0.83 -0.72 0.00 0.00 0.00 -0.23 -0.06 -0.08 -0.01 0.00 0.00 0.00 0.00 0.00 30.91
ID: VSI4_TRYBB AC: P26329 Len: 514 1:A 491 Sc: 30.91
32.84 -0.57 -0.83 -0.72 0.00 0.00 0.00 -0.23 -0.06 -0.08 -0.01 0.00 0.00 0.00 0.00 0.00 30.33
ID: VSI5_TRYBB AC: P26330 Len: 507 1:A 484 Sc: 30.33
33.90 -0.57 -0.83 -0.72 0.00 0.00 0.00 -0.02 -0.90 -0.08 -0.09 0.00 0.00 0.00 0.00 0.00 30.68
ID: VSI6_TRYBB AC: P06014 Len: 503 1:A 480 Sc: 30.68
22.15 0.00 0.00 0.00 0.00 0.00 0.00 -1.07 -0.30 0.00 0.00 0.00 0.00 0.00 0.00 0.00 20.77
ID: VSIB_TRYBB AC: P07208 Len: 471 1:B 454 Sc: 20.77
24.98 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.84 -0.50 -0.64 -12.00 0.00 0.00 0.00 0.00 11.00
ID: VSM0_TRYBB AC: P07209 Len: 72 1:C 50 Sc: 11.00
22.56 0.00 0.00 0.00 0.00 0.00 0.00 -0.93 -0.59 0.00 0.00 0.00 0.00 0.00 0.00 0.00 21.05
ID: VSM1_TRYBB AC: P26331 Len: 492 1:B 475 Sc: 21.05
21.71 0.00 0.00 -0.03 0.00 0.00 0.00 0.00 -0.13 0.00 0.00 0.00 0.00 0.00 0.00 0.00 21.55
ID: VSM2_TRYBB AC: P26332 Len: 476 1:B 459 Sc: 21.55
31.92 -0.57 -0.83 -0.72 0.00 0.00 0.00 -1.41 -0.45 -0.03 -0.01 0.00 0.00 0.00 0.00 0.00 27.89
ID: VSM4_TRYBB AC: P02896 Len: 526 1:B 503 Sc: 27.89
29.23 -0.63 -0.91 -0.53 0.00 0.00 0.00 0.00 -0.18 -0.74 -0.45 -12.00 0.00 0.00 -12.00 0.00 1.80
ID: VSM5_TRYBB AC: P26333 Len: 474 1:I 451 Sc: 1.80
29.97 -0.57 -0.83 -0.72 0.00 0.00 0.00 -2.92 -0.57 -0.08 -0.01 0.00 0.00 0.00 0.00 0.00 24.25
ID: VSM5_TRYBR AC: P21840 Len: 517 1:B 495 Sc: 24.25
32.59 -0.57 -0.83 -0.72 0.00 0.00 0.00 -1.41 -0.45 -0.03 -0.01 0.00 0.00 0.00 0.00 0.00 28.56
ID: VSM6_TRYBB AC: P26334 Len: 529 1:B 506 Sc: 28.56
20.32 0.00 0.00 -0.03 0.00 0.00 0.00 0.00 -0.13 0.00 0.00 0.00 0.00 0.00 0.00 0.00 20.17
ID: VSWA_TRYBR AC: P20946 Len: 471 1:B 454 Sc: 20.17
19.30 0.00 0.00 -0.03 0.00 0.00 0.00 0.00 -0.13 0.00 0.00 0.00 0.00 0.00 0.00 0.00 19.14
ID: VSWB_TRYBR AC: P20947 Len: 487 1:B 470 Sc: 19.14
18.03 0.00 0.00 0.00 0.00 0.00 0.00 0.00 0.00 -0.24 0.00 0.00 0.00 0.00 0.00 0.00 17.78
ID: VSY1_TRYCO AC: P20948 Len: 419 1:B 400 Sc: 17.78
-->end of list of found GPI-sites

   number of found GPI-sites 34
-->ReadSWEntry: End of File
   number of complete entries : 38
   number of failed entries : 0
   number of unselected entries : 131
-->CloseSWFile: Data file closed

# 
# 
# Normal termination of program proto.
# total program time: CPU 0:00:16.45 sec, elapsed time 0:00:20.00 sec
# 


Last modified: 12th June 2002